KSMoFinder知识图嵌入蛋白质和基因,用于预测人类酸盐的激酶
Manju Anandakrishnan1, Karen E Ross2, Chuming Chen1
1Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19713, United States.
Bioinformatics advances
|December 1, 2025
概括
KSMoFinder将蛋白质生物背景与序列动机相结合,用于优异的激酶基质预测. 这种新的方法通过比现有方法更准确地识别酸盐,提高了对细胞信号通路的理解.
科学领域:
- 生物化学 生化学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 蛋白激酶是细胞信号的关键调节者,通过酸化特定蛋白质残留物 (酸盐) 来调解生物过程.
- 目前的预测工具主要依赖于氨基酸序列动机,往往忽视了基底蛋白质的更广泛的生物背景.
- 精确识别酶-基质关系对于理解信号转导和疾病机制至关重要.
研究的目的:
- 开发KSMoFinder,一种用于预测酶-基质-动机关系的新型计算模型.
- 整合蛋白质生物背景与序列模式信息,以提高预测准确度.
- 将KSMoFinder的性能与现有的最先进的预测工具进行评估.
主要方法:
- KSMoFinder使用知识图来学习蛋白质,酶特异性动机和动机组成之间的语义关系.
- 蛋白质和图案以知识图嵌入式衍生出的矢量来表示.
- 一个监督深度学习分类器被训练使用这些矢量表示来预测酶-酸相互作用.
主要成果:
- 与现有的酶基质预测工具相比,KSMoFinder表现出优异的预测性能.
- 该模型在平衡测试数据集上实现ROC-AUC为0.851和PR-AUC为0.839.
- 知识图嵌入显著提高了比流行的蛋白质语言模型 (ProtT5,ESM2,ESM3) 的预测准确性.
结论:
- KSMoFinder有效地将生物背景集成到激酶基质预测中,优于基于动机的方法.
- 该模型提供了一个强大的工具,用于识别动机和基质蛋白级别的酶-酸关系.
- KSMoFinder推进了酶蛋白质组学和酶基质相互作用预测领域.
相关概念视频
Protein Kinases and Phosphatases
4.3K
4.3K
Protein Kinases and Phosphatases
14.9K
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
14.9K
Protein-protein Interfaces
14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
Protein-Protein Interfaces
4.4K
4.4K
Protein Networks
4.5K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.5K
Protein Networks
2.8K
2.8K


